I have automated web app which works fine on IE but when I try to execute same thing on Firefox it doesn't work(except opening the web page). I am using FF 14.0.1 and latest Ranorex . I am making sure that controls have focus before clicking, I checked my RXpath and it's correct and not browser specific and I am giving enough time delay. Am I missing something here?

Could you please send us a Ranorex Snapshot file of your web page when it is opened in Firefox and your repository file?
This would help us to analyze the issue.
If you like you can also send it to our support mail address: [email protected]
Following link will show you how to generate a snapshot file:Creating Ranorex Snapshot Files.

so seems like problem was with my code. On opening the web page I get the certification error. I have written a small user code where I check if that particular link is null then check if it's visible, if it is visible then click on it.

This certification error page looks diff on FF, Safari and Chrome. This was the code which was breaking my test(and nothing was happening). I removed the code and things seems to work fine.

As Artur said if you want to check if the specific element of your AUT exists you have to use one of the methods of the repository item.
If you check if the repo item is != null, you just check if the repository item object itself exists and not if the element of your web app exists.